Targeted Proteomics and Support Vector Classification Reveal Potential Biomarkers for the Early Detection of High-grade Serous Ovarian Cancer

Cooper, T. T.; Dieters-Castator, D. Z.; Liu, J.; Siegers, G. M.; Pink, D.; Lewis, J. D.; Fu, Y.; Steed, H.; Lajoie, G. A.; Postovit, L. M.

doi:10.1101/2022.03.31.486596

bioRxiv · 10.1101/2022.03.31.486596

Targeted Proteomics and Support Vector Classification Reveal Potential Biomarkers for the Early Detection of High-grade Serous Ovarian Cancer

Cooper, T. T.·Dieters-Castator, D. Z.·Liu, J.·Siegers, G. M.·Pink, D.·Lewis, J. D.·Fu, Y.·Steed, H.·Lajoie, G. A.·Postovit, L. M.

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Abstract

PurposeThe five-year prognosis for patients with late-stage high-grade serous carcinoma (HGSC) remains dismal, underscoring the critical need for identifying early-stage biomarkers. This study explores the potential of extracellular vesicles (EVs) circulating in blood, which are believed to harbor proteomic cargo reflective of the HGSC microenvironment, as a source for biomarker discovery. Experimental DesignWe conducted a comprehensive proteomic profiling of EVs isolated from blood plasma, ascites, and cell lines of patients, employing both data-dependent (DDA) and data-independent acquisition (DIA) methods to construct a spectral library tailored for targeted proteomics. Our investigation aimed at uncovering novel biomarkers for the early detection of HGSC by comparing the proteomic signatures of EVs from women with HGSC to those with benign gynecological conditions. The initial cohort, comprising 9-10 donors, utilized DDA proteomics for spectral library development. The subsequent cohort, involving 30 HGSC patients and 30 control subjects, employed DIA proteomics for a similar purpose. Support vector machine (SVM) classification was applied in both cohorts to identify combinatorial biomarkers with high specificity and sensitivity (ROC-AUC > 0.90). ResultsNotably, MUC1 emerged as a significant biomarker in both cohorts when used in combination with additional biomarkers. Validation through an ELISA assay on a subset of benign (n=18), Stage I (n=9), and stage II (n=9) plasma samples corroborated the diagnostic utility of MUC1 in the early-stage detection of HGSC. ConclusionsThis study highlights the value of EV-based proteomic analysis in the discovery of combinatorial biomarkers for early ovarian cancer detection.

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Cooper, T. T., Dieters-Castator, D. Z., Liu, J., Siegers, G. M., Pink, D., Lewis, J. D., Fu, Y., Steed, H., Lajoie, G. A., Postovit, L. M.. 2022-04-01. Targeted Proteomics and Support Vector Classification Reveal Potential Biomarkers for the Early Detection of High-grade Serous Ovarian Cancer. https://doi.org/10.1101/2022.03.31.486596

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